The recent completion of the Saccharaomyces cerevisae yeast genome project provides biologists with a resource for identifying protein components of complex macromolecular assemblages that mediate processes such as transcriptional regulation, RNA splicing and signal transduction. To fully exploit this resource, rapid methods are needed to correlate mature proteins in such assemblages with their corresponding gene sequences. Here we demonstrate the use of matrix-assisted laser desorption/ionization ion trap tandem mass spectrometry (MALDI-ITMS) in combination with database searching of the yeast genome to identify proteins interacting with the RNA polymerase II carboxyl terminal repeat domain. Eleven proteins were identified in two days. Five are known components of the RNA polymerase 11 holoenzyme, and four correspond to open reading frames with unknown functions. The identification of ACT3 and RRN7 as CTD-binding proteins suggests a link between the class II transcriptional apparatus and actin-related functions as well as a common regulatory mechanism conserved between RNA polymerases I and Il. A paper describing this work was published (Qin et al, Anal. Chem. 69, 3995-4001, 1997.